Chemical Components in the PDB

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RB0 : Summary

Code

RB0

One-letter code

X

Molecule name

D-ribitol

Systematic names

ProgramVersionName
ACDLabs 12.01 D-ribitol
OpenEye OEToolkits 1.7.6 (2S,4R)-pentane-1,2,3,4,5-pentol

Formula

C5 H12 O5

Formal charge

0

Molecular weight

152.146 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 OC(CO)C(O)C(O)CO
SMILES CACTVS 3.370 OC[CH](O)[CH](O)[CH](O)CO
SMILES OpenEye OEToolkits 1.7.6 C(C(C(C(CO)O)O)O)O
Canonical SMILES CACTVS 3.370 OC[C@H](O)[C@H](O)[C@H](O)CO
Canonical SMILES OpenEye OEToolkits 1.7.6 C([C@H](C([C@H](CO)O)O)O)O

IUPAC InChI

InChI=1S/C5H12O5/c6-1-3(8)5(10)4(9)2-7/h3-10H,1-2H2/t3-,4+,5-

IUPAC InChI key

HEBKCHPVOIAQTA-ZXFHETKHSA-N
RB0

wwPDB Information

Atom count

22 (10 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

ATOMS

Is modified

No

Standard parent

Not Assigned

Defined at

2012-05-17

Last modified at

2012-05-25

Status

Released

Obsoleted

Not Assigned



RB0 : Atoms of Molecule

Total Number of Atoms: 22
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C1 C C1 N N N 0 -2.495 -0.663 0.134
2 O1 O O1 N N N 0 -3.665 0.103 0.429
3 C2 C C2 S N N 0 -1.249 0.166 0.453
4 O2 O O2 N N N 0 -1.192 1.296 -0.421
5 C3 C C3 S N N 0 0.0 -0.695 0.256
6 O3 O O3 N N N 0 0.0 -1.238 -1.066
7 C4 C C4 R N N 0 1.249 0.166 0.453
8 O4 O O4 N N N 0 1.192 1.296 -0.421
9 C5 C C5 N N N 0 2.495 -0.663 0.134
10 O5 O O5 N N N 0 3.665 0.103 0.429
11 H1 H H1 N N N 0 -2.493 -1.57 0.738
12 H1A H H1A N N N 0 -2.493 -0.93 -0.923
13 HO1 H HO1 N N N 0 -4.494 -0.361 0.251
14 H2 H H2 N N N 0 -1.295 0.508 1.487
15 HO2 H HO2 N N N 0 -1.149 1.066 -1.359
16 H3 H H3 N N N 0 0.0 -1.507 0.983
17 HO3 H HO3 N N N 0 0.0 -0.571 -1.766
18 H4 H H4 N N N 0 1.295 0.508 1.487
19 HO4 H HO4 N N N 0 1.149 1.066 -1.359
20 H5 H H5 N N N 0 2.493 -1.57 0.738
21 H5A H H5A N N N 0 2.493 -0.93 -0.923
22 HO5 H HO5 N N N 0 4.494 -0.361 0.251



RB0 : Chemical Bonds

Total Number of Bonds: 21
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C1 O1 C O sing 1.43 N N
2 C1 C2 C C sing 1.53 N N
3 C2 O2 C O sing 1.43 N N
4 C2 C3 C C sing 1.53 N N
5 C3 O3 C O sing 1.43 N N
6 C3 C4 C C sing 1.53 N N
7 C4 O4 C O sing 1.43 N N
8 C4 C5 C C sing 1.53 N N
9 C5 O5 C O sing 1.43 N N
10 C1 H1 C H sing 1.09 N N
11 C1 H1A C H sing 1.09 N N
12 O1 HO1 O H sing 0.97 N N
13 C2 H2 C H sing 1.09 N N
14 O2 HO2 O H sing 0.97 N N
15 C3 H3 C H sing 1.09 N N
16 O3 HO3 O H sing 0.97 N N
17 C4 H4 C H sing 1.09 N N
18 O4 HO4 O H sing 0.97 N N
19 C5 H5 C H sing 1.09 N N
20 C5 H5A C H sing 1.09 N N
21 O5 HO5 O H sing 0.97 N N



RB0 : Used in PDB Entries

Total Number of PDB Entries: 6
Ligand Code PDB Entry ID Type Total Distinct
RB0 4f2d Open in New Window Bound ligand 3 1
RB0 4q0s Open in New Window Bound ligand 2 1
RB0 5iai Open in New Window Bound ligand 1 1
RB0 6kaj Open in New Window Bound ligand 4 1
RB0 6kam Open in New Window Bound ligand 4 1
RB0 7cyy Open in New Window Bound ligand 6 1